Certain studies previously pointed out that treating pregnant women with antidepressants may increase risks of congenital anomalies in their children. However, to date, the study results are not conclusive. Furthermore, most studies have been performed using data from Western countries; therefore, we examined this association using Japanese data. This retrospective cohort study was based on claims data of mothers and their children from January 2005 to July 2014, obtained from the JMDC Inc. Information on antidepressant prescriptions was extracted from the database. Children were followed up from birth through July 2014 or until their withdrawal from the database and were identified for obtaining information on their congenital anomalies. We used logistic regression analysis to evaluate the association between maternal antidepressant use during pregnancy and the children's congenital anomalies. Of 53 864 eligible pairs of mothers and children, 53 697 pairs met the study criteria. No increased risk of total congenital anomalies in children whose mothers used antidepressants of any type during the first trimester of pregnancy was found in the analysis (adjusted analysis with confounders, odds ratio: 0.86; 95% confidence interval: 0.52, 1.42). In addition, there was no increased risk of organ specific anomalies in the analysis by type of antidepressant. We found no increased risk of congenital anomalies in children whose mothers used antidepressants during the first trimester of pregnancy compared to that of non-users based on the Japanese claims data. Additional studies are necessary to further clarify the association between antidepressant use during pregnancy and congenital anomalies in children.